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Opened 4 weeks ago
Closed 4 weeks ago
#19120 closed defect (not a bug)
H-Bonds: acc_phi_psi() bad number of arguments
| Reported by: | Owned by: | Eric Pettersen | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Structure Analysis | Version: | |
| Keywords: | Cc: | Tom Goddard | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: Windows-10-10.0.26100
ChimeraX Version: 1.10.1 (2025-07-24 20:15:27 UTC)
Description
Replace this text with list of actions that caused this problem to occur
Log:
UCSF ChimeraX version: 1.10.1 (2025-07-24)
© 2016-2025 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open C:/Users/user/Downloads/model_2.pdb
Summary of feedback from opening C:/Users/user/Downloads/model_2.pdb
---
warnings | Ignored bad PDB record found on line 1
REMARK Number: 2
Ignored bad PDB record found on line 2
REMARK Ligand: lig_68ecca2783a47.pdb
Ignored bad PDB record found on line 3
REMARK Contact: 0 0 0
Ignored bad PDB record found on line 4
REMARK Score: -239.19
Ignored bad PDB record found on line 5
REMARK RMSD: 51.40
Chain information for model_2.pdb #1
---
Chain | Description
A | No description available
A | No description available
Computing secondary structure
> ui tool show H-Bonds
> hbonds reveal true
/A DG 4 O4' has bad number of bonds (5)
/A DT 9 O5' has bad number of bonds (5)
/A DT 9 O4' has bad number of bonds (5)
donor: /A DG 1 N1 acceptor: /A DG 4 N7
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\hbonds\tool.py", line 53, in run_hbonds
run(self.session, " ".join(self.gui.get_command()))
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\core\commands\run.py", line 49, in run
results = command.run(text, log=log, return_json=return_json)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3221, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\hbonds\cmd.py", line 94, in cmd_hbonds
result = hb_func(session, struct_info, dist_slop=dist_slop,
angle_slop=angle_slop, **base_kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\hbonds\hbond.py", line 615, in find_hbonds
if not geom_func(donor_atom, donor_hyds, *args):
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
TypeError: acc_phi_psi() takes 8 positional arguments but 10 were given
TypeError: acc_phi_psi() takes 8 positional arguments but 10 were given
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\hbonds\hbond.py", line 615, in find_hbonds
if not geom_func(donor_atom, donor_hyds, *args):
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
> ui tool show ViewDockX
No suitable models found for ViewDockX
> ui tool show "Find Cavities"
pyKVFinder module not installed; fetching from PyPi repository...
'pip install pyKVFinder' failed. Error from pip:
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\kvfinder\\__init__.py", line 48, in check_pyKVFinder
import pyKVFinder
ModuleNotFoundError: No module named 'pyKVFinder'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\core\toolshed\info.py", line 571, in start_tool
ti = api._api_caller.start_tool(api, session, self, tool_info)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\core\toolshed\\__init__.py", line 1399, in start_tool
return cls._get_func(api, "start_tool")(session, ti.name)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\kvfinder\\__init__.py", line 42, in start_tool
check_pyKVFinder(session.logger)
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\kvfinder\\__init__.py", line 54, in check_pyKVFinder
run(logger.session, pip_cmd, log=False)
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\core\commands\run.py", line 49, in run
results = command.run(text, log=log, return_json=return_json)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3221, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\core\commands\pip.py", line 88, in pip
run_logged_pip(pip_cmd, session.logger)
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\core\python_utils.py", line 143, in run_logged_pip
raise RuntimeError(s)
RuntimeError
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\ui\gui.py", line 1891, in <lambda>
run(ses, "ui tool show %s" % StringArg.unparse(tool_name)))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\core\commands\run.py", line 49, in run
results = command.run(text, log=log, return_json=return_json)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3221, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\ui\cmd.py", line 219, in ui_tool_show
return bi.start_tool(session, name)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\core\toolshed\info.py", line 578, in start_tool
raise ToolshedError(
chimerax.core.toolshed.ToolshedError: start_tool() failed for tool Find
Cavities in bundle ChimeraX-KVFinder:
chimerax.core.toolshed.ToolshedError: start_tool() failed for tool Find
Cavities in bundle ChimeraX-KVFinder:
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\core\toolshed\info.py", line 578, in start_tool
raise ToolshedError(
See log for complete Python traceback.
> ui tool show Clashes
> clashes ignoreHiddenModels true
75 clashes
> ui tool show "Find Cavities"
pyKVFinder module not installed; fetching from PyPi repository...
pyKVFinder module installed from PyPi repository.
> kvfinder
15 cavities found for model_2.pdb #1
model_2.pdb Cavities
---
ID | | Volume | Area | Points | Maximum
Depth | Average
Depth
1.2.6 | | 1545.7 | 986.13 | 7156 | 6.49 | 1.63
1.2.2 | | 97.63 | 95.32 | 452 | 3.55 | 1.18
1.2.7 | | 44.5 | 60.35 | 206 | 3.06 | 1.04
1.2.1 | | 31.97 | 61.64 | 148 | 3.65 | 1.22
1.2.12 | | 27 | 36.37 | 125 | 1.8 | 0.5
1.2.3 | | 25.92 | 33.47 | 120 | 1.9 | 0.62
1.2.8 | | 23.98 | 41.38 | 111 | 3.5 | 1.56
1.2.4 | | 21.82 | 29.63 | 101 | 1.34 | 0.32
1.2.10 | | 21.38 | 29.71 | 99 | 1.2 | 0.3
1.2.14 | | 16.85 | 32.3 | 78 | 0 | 0
1.2.9 | | 15.77 | 26.99 | 73 | 1.7 | 0.67
1.2.13 | | 12.31 | 29.54 | 57 | 0 | 0
1.2.11 | | 11.02 | 24.45 | 51 | 0.85 | 0.22
1.2.5 | | 9.5 | 18.26 | 44 | 1.2 | 0.37
1.2.15 | | 7.56 | 11.02 | 35 | 0.85 | 0.23
> kvfinder
15 cavities found for model_2.pdb #1
model_2.pdb Cavities
---
ID | | Volume | Area | Points | Maximum
Depth | Average
Depth
1.2.6 | | 1545.7 | 986.13 | 7156 | 6.49 | 1.63
1.2.2 | | 97.63 | 95.32 | 452 | 3.55 | 1.18
1.2.7 | | 44.5 | 60.35 | 206 | 3.06 | 1.04
1.2.1 | | 31.97 | 61.64 | 148 | 3.65 | 1.22
1.2.12 | | 27 | 36.37 | 125 | 1.8 | 0.5
1.2.3 | | 25.92 | 33.47 | 120 | 1.9 | 0.62
1.2.8 | | 23.98 | 41.38 | 111 | 3.5 | 1.56
1.2.4 | | 21.82 | 29.63 | 101 | 1.34 | 0.32
1.2.10 | | 21.38 | 29.71 | 99 | 1.2 | 0.3
1.2.14 | | 16.85 | 32.3 | 78 | 0 | 0
1.2.9 | | 15.77 | 26.99 | 73 | 1.7 | 0.67
1.2.13 | | 12.31 | 29.54 | 57 | 0 | 0
1.2.11 | | 11.02 | 24.45 | 51 | 0.85 | 0.22
1.2.5 | | 9.5 | 18.26 | 44 | 1.2 | 0.37
1.2.15 | | 7.56 | 11.02 | 35 | 0.85 | 0.23
> kvfinder
15 cavities found for model_2.pdb #1
model_2.pdb Cavities
---
ID | | Volume | Area | Points | Maximum
Depth | Average
Depth
1.2.6 | | 1545.7 | 986.13 | 7156 | 6.49 | 1.63
1.2.2 | | 97.63 | 95.32 | 452 | 3.55 | 1.18
1.2.7 | | 44.5 | 60.35 | 206 | 3.06 | 1.04
1.2.1 | | 31.97 | 61.64 | 148 | 3.65 | 1.22
1.2.12 | | 27 | 36.37 | 125 | 1.8 | 0.5
1.2.3 | | 25.92 | 33.47 | 120 | 1.9 | 0.62
1.2.8 | | 23.98 | 41.38 | 111 | 3.5 | 1.56
1.2.4 | | 21.82 | 29.63 | 101 | 1.34 | 0.32
1.2.10 | | 21.38 | 29.71 | 99 | 1.2 | 0.3
1.2.14 | | 16.85 | 32.3 | 78 | 0 | 0
1.2.9 | | 15.77 | 26.99 | 73 | 1.7 | 0.67
1.2.13 | | 12.31 | 29.54 | 57 | 0 | 0
1.2.11 | | 11.02 | 24.45 | 51 | 0.85 | 0.22
1.2.5 | | 9.5 | 18.26 | 44 | 1.2 | 0.37
1.2.15 | | 7.56 | 11.02 | 35 | 0.85 | 0.23
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 34, in data
val = col.display_value(item)
^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 886, in display_value
val = self.value(instance)
^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 903, in value
return self.data_fetch(instance)
^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\kvfinder\tool.py", line 201, in color_func
if s.display and s.atoms.displays.any():
^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\atomic\structure.py", line 529, in _get_display
return Model.display.fget(self)
^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 389, in get_display
return self._any_displayed_positions and len(self._positions) > 0
^^^^^^^^^^^^^^^^^^^^
TypeError: object of type 'NoneType' has no len()
TypeError: object of type 'NoneType' has no len()
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 389, in get_display
return self._any_displayed_positions and len(self._positions) > 0
^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 34, in data
val = col.display_value(item)
^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 886, in display_value
val = self.value(instance)
^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 903, in value
return self.data_fetch(instance)
^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\kvfinder\tool.py", line 201, in color_func
if s.display and s.atoms.displays.any():
^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\atomic\structure.py", line 529, in _get_display
return Model.display.fget(self)
^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 389, in get_display
return self._any_displayed_positions and len(self._positions) > 0
^^^^^^^^^^^^^^^^^^^^
TypeError: object of type 'NoneType' has no len()
TypeError: object of type 'NoneType' has no len()
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 389, in get_display
return self._any_displayed_positions and len(self._positions) > 0
^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 34, in data
val = col.display_value(item)
^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 886, in display_value
val = self.value(instance)
^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 903, in value
return self.data_fetch(instance)
^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\kvfinder\tool.py", line 201, in color_func
if s.display and s.atoms.displays.any():
^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\atomic\structure.py", line 529, in _get_display
return Model.display.fget(self)
^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 389, in get_display
return self._any_displayed_positions and len(self._positions) > 0
^^^^^^^^^^^^^^^^^^^^
TypeError: object of type 'NoneType' has no len()
TypeError: object of type 'NoneType' has no len()
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 389, in get_display
return self._any_displayed_positions and len(self._positions) > 0
^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 34, in data
val = col.display_value(item)
^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 886, in display_value
val = self.value(instance)
^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 903, in value
return self.data_fetch(instance)
^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\kvfinder\tool.py", line 201, in color_func
if s.display and s.atoms.displays.any():
^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\atomic\structure.py", line 529, in _get_display
return Model.display.fget(self)
^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 389, in get_display
return self._any_displayed_positions and len(self._positions) > 0
^^^^^^^^^^^^^^^^^^^^
TypeError: object of type 'NoneType' has no len()
TypeError: object of type 'NoneType' has no len()
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 389, in get_display
return self._any_displayed_positions and len(self._positions) > 0
^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 34, in data
val = col.display_value(item)
^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 886, in display_value
val = self.value(instance)
^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 903, in value
return self.data_fetch(instance)
^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\kvfinder\tool.py", line 201, in color_func
if s.display and s.atoms.displays.any():
^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\atomic\structure.py", line 529, in _get_display
return Model.display.fget(self)
^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 389, in get_display
return self._any_displayed_positions and len(self._positions) > 0
^^^^^^^^^^^^^^^^^^^^
TypeError: object of type 'NoneType' has no len()
TypeError: object of type 'NoneType' has no len()
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 389, in get_display
return self._any_displayed_positions and len(self._positions) > 0
^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 34, in data
val = col.display_value(item)
^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 886, in display_value
val = self.value(instance)
^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 903, in value
return self.data_fetch(instance)
^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\kvfinder\tool.py", line 201, in color_func
if s.display and s.atoms.displays.any():
^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\atomic\structure.py", line 529, in _get_display
return Model.display.fget(self)
^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 389, in get_display
return self._any_displayed_positions and len(self._positions) > 0
^^^^^^^^^^^^^^^^^^^^
TypeError: object of type 'NoneType' has no len()
TypeError: object of type 'NoneType' has no len()
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 389, in get_display
return self._any_displayed_positions and len(self._positions) > 0
^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 34, in data
val = col.display_value(item)
^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 886, in display_value
val = self.value(instance)
^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 903, in value
return self.data_fetch(instance)
^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\kvfinder\tool.py", line 201, in color_func
if s.display and s.atoms.displays.any():
^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\atomic\structure.py", line 529, in _get_display
return Model.display.fget(self)
^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 389, in get_display
return self._any_displayed_positions and len(self._positions) > 0
^^^^^^^^^^^^^^^^^^^^
TypeError: object of type 'NoneType' has no len()
TypeError: object of type 'NoneType' has no len()
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 389, in get_display
return self._any_displayed_positions and len(self._positions) > 0
^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 34, in data
val = col.display_value(item)
^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 886, in display_value
val = self.value(instance)
^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 903, in value
return self.data_fetch(instance)
^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\kvfinder\tool.py", line 201, in color_func
if s.display and s.atoms.displays.any():
^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\atomic\structure.py", line 529, in _get_display
return Model.display.fget(self)
^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 389, in get_display
return self._any_displayed_positions and len(self._positions) > 0
^^^^^^^^^^^^^^^^^^^^
TypeError: object of type 'NoneType' has no len()
TypeError: object of type 'NoneType' has no len()
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 389, in get_display
return self._any_displayed_positions and len(self._positions) > 0
^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 34, in data
val = col.display_value(item)
^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 886, in display_value
val = self.value(instance)
^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 903, in value
return self.data_fetch(instance)
^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\kvfinder\tool.py", line 201, in color_func
if s.display and s.atoms.displays.any():
^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\atomic\structure.py", line 529, in _get_display
return Model.display.fget(self)
^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 389, in get_display
return self._any_displayed_positions and len(self._positions) > 0
^^^^^^^^^^^^^^^^^^^^
TypeError: object of type 'NoneType' has no len()
TypeError: object of type 'NoneType' has no len()
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 389, in get_display
return self._any_displayed_positions and len(self._positions) > 0
^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 34, in data
val = col.display_value(item)
^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 886, in display_value
val = self.value(instance)
^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 903, in value
return self.data_fetch(instance)
^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\kvfinder\tool.py", line 201, in color_func
if s.display and s.atoms.displays.any():
^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\atomic\structure.py", line 529, in _get_display
return Model.display.fget(self)
^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 389, in get_display
return self._any_displayed_positions and len(self._positions) > 0
^^^^^^^^^^^^^^^^^^^^
TypeError: object of type 'NoneType' has no len()
TypeError: object of type 'NoneType' has no len()
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 389, in get_display
return self._any_displayed_positions and len(self._positions) > 0
^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 34, in data
val = col.display_value(item)
^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 886, in display_value
val = self.value(instance)
^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 903, in value
return self.data_fetch(instance)
^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\kvfinder\tool.py", line 201, in color_func
if s.display and s.atoms.displays.any():
^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\atomic\structure.py", line 529, in _get_display
return Model.display.fget(self)
^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 389, in get_display
return self._any_displayed_positions and len(self._positions) > 0
^^^^^^^^^^^^^^^^^^^^
TypeError: object of type 'NoneType' has no len()
TypeError: object of type 'NoneType' has no len()
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 389, in get_display
return self._any_displayed_positions and len(self._positions) > 0
^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 34, in data
val = col.display_value(item)
^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 886, in display_value
val = self.value(instance)
^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 903, in value
return self.data_fetch(instance)
^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\kvfinder\tool.py", line 201, in color_func
if s.display and s.atoms.displays.any():
^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\atomic\structure.py", line 529, in _get_display
return Model.display.fget(self)
^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 389, in get_display
return self._any_displayed_positions and len(self._positions) > 0
^^^^^^^^^^^^^^^^^^^^
TypeError: object of type 'NoneType' has no len()
TypeError: object of type 'NoneType' has no len()
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 389, in get_display
return self._any_displayed_positions and len(self._positions) > 0
^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 34, in data
val = col.display_value(item)
^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 886, in display_value
val = self.value(instance)
^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 903, in value
return self.data_fetch(instance)
^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\kvfinder\tool.py", line 201, in color_func
if s.display and s.atoms.displays.any():
^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\atomic\structure.py", line 529, in _get_display
return Model.display.fget(self)
^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 389, in get_display
return self._any_displayed_positions and len(self._positions) > 0
^^^^^^^^^^^^^^^^^^^^
TypeError: object of type 'NoneType' has no len()
TypeError: object of type 'NoneType' has no len()
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 389, in get_display
return self._any_displayed_positions and len(self._positions) > 0
^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 34, in data
val = col.display_value(item)
^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 886, in display_value
val = self.value(instance)
^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 903, in value
return self.data_fetch(instance)
^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\kvfinder\tool.py", line 201, in color_func
if s.display and s.atoms.displays.any():
^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\atomic\structure.py", line 529, in _get_display
return Model.display.fget(self)
^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 389, in get_display
return self._any_displayed_positions and len(self._positions) > 0
^^^^^^^^^^^^^^^^^^^^
TypeError: object of type 'NoneType' has no len()
TypeError: object of type 'NoneType' has no len()
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 389, in get_display
return self._any_displayed_positions and len(self._positions) > 0
^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 34, in data
val = col.display_value(item)
^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 886, in display_value
val = self.value(instance)
^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 903, in value
return self.data_fetch(instance)
^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\kvfinder\tool.py", line 201, in color_func
if s.display and s.atoms.displays.any():
^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\atomic\structure.py", line 529, in _get_display
return Model.display.fget(self)
^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 389, in get_display
return self._any_displayed_positions and len(self._positions) > 0
^^^^^^^^^^^^^^^^^^^^
TypeError: object of type 'NoneType' has no len()
TypeError: object of type 'NoneType' has no len()
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 389, in get_display
return self._any_displayed_positions and len(self._positions) > 0
^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 34, in data
val = col.display_value(item)
^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 886, in display_value
val = self.value(instance)
^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 903, in value
return self.data_fetch(instance)
^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\kvfinder\tool.py", line 201, in color_func
if s.display and s.atoms.displays.any():
^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\atomic\structure.py", line 529, in _get_display
return Model.display.fget(self)
^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 389, in get_display
return self._any_displayed_positions and len(self._positions) > 0
^^^^^^^^^^^^^^^^^^^^
TypeError: object of type 'NoneType' has no len()
TypeError: object of type 'NoneType' has no len()
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 389, in get_display
return self._any_displayed_positions and len(self._positions) > 0
^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 34, in data
val = col.display_value(item)
^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 886, in display_value
val = self.value(instance)
^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 903, in value
return self.data_fetch(instance)
^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\kvfinder\tool.py", line 201, in color_func
if s.display and s.atoms.displays.any():
^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\atomic\structure.py", line 529, in _get_display
return Model.display.fget(self)
^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 389, in get_display
return self._any_displayed_positions and len(self._positions) > 0
^^^^^^^^^^^^^^^^^^^^
TypeError: object of type 'NoneType' has no len()
TypeError: object of type 'NoneType' has no len()
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 389, in get_display
return self._any_displayed_positions and len(self._positions) > 0
^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 34, in data
val = col.display_value(item)
^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 886, in display_value
val = self.value(instance)
^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 903, in value
return self.data_fetch(instance)
^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\kvfinder\tool.py", line 201, in color_func
if s.display and s.atoms.displays.any():
^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\atomic\structure.py", line 529, in _get_display
return Model.display.fget(self)
^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 389, in get_display
return self._any_displayed_positions and len(self._positions) > 0
^^^^^^^^^^^^^^^^^^^^
TypeError: object of type 'NoneType' has no len()
TypeError: object of type 'NoneType' has no len()
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 389, in get_display
return self._any_displayed_positions and len(self._positions) > 0
^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 34, in data
val = col.display_value(item)
^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 886, in display_value
val = self.value(instance)
^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 903, in value
return self.data_fetch(instance)
^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\kvfinder\tool.py", line 201, in color_func
if s.display and s.atoms.displays.any():
^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\atomic\structure.py", line 529, in _get_display
return Model.display.fget(self)
^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 389, in get_display
return self._any_displayed_positions and len(self._positions) > 0
^^^^^^^^^^^^^^^^^^^^
TypeError: object of type 'NoneType' has no len()
TypeError: object of type 'NoneType' has no len()
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 389, in get_display
return self._any_displayed_positions and len(self._positions) > 0
^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 34, in data
val = col.display_value(item)
^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 886, in display_value
val = self.value(instance)
^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 903, in value
return self.data_fetch(instance)
^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\kvfinder\tool.py", line 201, in color_func
if s.display and s.atoms.displays.any():
^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\atomic\structure.py", line 529, in _get_display
return Model.display.fget(self)
^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 389, in get_display
return self._any_displayed_positions and len(self._positions) > 0
^^^^^^^^^^^^^^^^^^^^
TypeError: object of type 'NoneType' has no len()
TypeError: object of type 'NoneType' has no len()
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 389, in get_display
return self._any_displayed_positions and len(self._positions) > 0
^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 34, in data
val = col.display_value(item)
^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 886, in display_value
val = self.value(instance)
^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 903, in value
return self.data_fetch(instance)
^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\kvfinder\tool.py", line 201, in color_func
if s.display and s.atoms.displays.any():
^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\atomic\structure.py", line 529, in _get_display
return Model.display.fget(self)
^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 389, in get_display
return self._any_displayed_positions and len(self._positions) > 0
^^^^^^^^^^^^^^^^^^^^
TypeError: object of type 'NoneType' has no len()
TypeError: object of type 'NoneType' has no len()
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 389, in get_display
return self._any_displayed_positions and len(self._positions) > 0
^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 34, in data
val = col.display_value(item)
^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 886, in display_value
val = self.value(instance)
^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 903, in value
return self.data_fetch(instance)
^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\kvfinder\tool.py", line 201, in color_func
if s.display and s.atoms.displays.any():
^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\atomic\structure.py", line 529, in _get_display
return Model.display.fget(self)
^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 389, in get_display
return self._any_displayed_positions and len(self._positions) > 0
^^^^^^^^^^^^^^^^^^^^
TypeError: object of type 'NoneType' has no len()
TypeError: object of type 'NoneType' has no len()
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 389, in get_display
return self._any_displayed_positions and len(self._positions) > 0
^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 34, in data
val = col.display_value(item)
^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 886, in display_value
val = self.value(instance)
^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 903, in value
return self.data_fetch(instance)
^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\kvfinder\tool.py", line 201, in color_func
if s.display and s.atoms.displays.any():
^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\atomic\structure.py", line 529, in _get_display
return Model.display.fget(self)
^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 389, in get_display
return self._any_displayed_positions and len(self._positions) > 0
^^^^^^^^^^^^^^^^^^^^
TypeError: object of type 'NoneType' has no len()
TypeError: object of type 'NoneType' has no len()
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 389, in get_display
return self._any_displayed_positions and len(self._positions) > 0
^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 34, in data
val = col.display_value(item)
^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 886, in display_value
val = self.value(instance)
^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 903, in value
return self.data_fetch(instance)
^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\kvfinder\tool.py", line 201, in color_func
if s.display and s.atoms.displays.any():
^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\atomic\structure.py", line 529, in _get_display
return Model.display.fget(self)
^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 389, in get_display
return self._any_displayed_positions and len(self._positions) > 0
^^^^^^^^^^^^^^^^^^^^
TypeError: object of type 'NoneType' has no len()
TypeError: object of type 'NoneType' has no len()
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 389, in get_display
return self._any_displayed_positions and len(self._positions) > 0
^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 34, in data
val = col.display_value(item)
^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 886, in display_value
val = self.value(instance)
^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 903, in value
return self.data_fetch(instance)
^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\kvfinder\tool.py", line 201, in color_func
if s.display and s.atoms.displays.any():
^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\atomic\structure.py", line 529, in _get_display
return Model.display.fget(self)
^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 389, in get_display
return self._any_displayed_positions and len(self._positions) > 0
^^^^^^^^^^^^^^^^^^^^
TypeError: object of type 'NoneType' has no len()
TypeError: object of type 'NoneType' has no len()
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 389, in get_display
return self._any_displayed_positions and len(self._positions) > 0
^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 34, in data
val = col.display_value(item)
^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 886, in display_value
val = self.value(instance)
^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 903, in value
return self.data_fetch(instance)
^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\kvfinder\tool.py", line 201, in color_func
if s.display and s.atoms.displays.any():
^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\atomic\structure.py", line 529, in _get_display
return Model.display.fget(self)
^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 389, in get_display
return self._any_displayed_positions and len(self._positions) > 0
^^^^^^^^^^^^^^^^^^^^
TypeError: object of type 'NoneType' has no len()
TypeError: object of type 'NoneType' has no len()
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 389, in get_display
return self._any_displayed_positions and len(self._positions) > 0
^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 34, in data
val = col.display_value(item)
^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 886, in display_value
val = self.value(instance)
^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 903, in value
return self.data_fetch(instance)
^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\kvfinder\tool.py", line 201, in color_func
if s.display and s.atoms.displays.any():
^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\atomic\structure.py", line 529, in _get_display
return Model.display.fget(self)
^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 389, in get_display
return self._any_displayed_positions and len(self._positions) > 0
^^^^^^^^^^^^^^^^^^^^
TypeError: object of type 'NoneType' has no len()
TypeError: object of type 'NoneType' has no len()
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 389, in get_display
return self._any_displayed_positions and len(self._positions) > 0
^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 34, in data
val = col.display_value(item)
^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 886, in display_value
val = self.value(instance)
^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 903, in value
return self.data_fetch(instance)
^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\kvfinder\tool.py", line 201, in color_func
if s.display and s.atoms.displays.any():
^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\atomic\structure.py", line 529, in _get_display
return Model.display.fget(self)
^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 389, in get_display
return self._any_displayed_positions and len(self._positions) > 0
^^^^^^^^^^^^^^^^^^^^
TypeError: object of type 'NoneType' has no len()
TypeError: object of type 'NoneType' has no len()
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 389, in get_display
return self._any_displayed_positions and len(self._positions) > 0
^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 34, in data
val = col.display_value(item)
^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 886, in display_value
val = self.value(instance)
^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 903, in value
return self.data_fetch(instance)
^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\kvfinder\tool.py", line 201, in color_func
if s.display and s.atoms.displays.any():
^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\atomic\structure.py", line 529, in _get_display
return Model.display.fget(self)
^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 389, in get_display
return self._any_displayed_positions and len(self._positions) > 0
^^^^^^^^^^^^^^^^^^^^
TypeError: object of type 'NoneType' has no len()
TypeError: object of type 'NoneType' has no len()
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 389, in get_display
return self._any_displayed_positions and len(self._positions) > 0
^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 34, in data
val = col.display_value(item)
^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 886, in display_value
val = self.value(instance)
^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 903, in value
return self.data_fetch(instance)
^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\kvfinder\tool.py", line 201, in color_func
if s.display and s.atoms.displays.any():
^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\atomic\structure.py", line 529, in _get_display
return Model.display.fget(self)
^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 389, in get_display
return self._any_displayed_positions and len(self._positions) > 0
^^^^^^^^^^^^^^^^^^^^
TypeError: object of type 'NoneType' has no len()
TypeError: object of type 'NoneType' has no len()
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 389, in get_display
return self._any_displayed_positions and len(self._positions) > 0
^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\bug_reporter\tool.py", line 192, in <lambda>
sb.clicked.connect(lambda e: self.submit())
^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\bug_reporter\tool.py", line 249, in submit
self.status("Contacting CGL....", color="blue")
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\bug_reporter\tool.py", line 311, in status
self.result.setText(text)
RuntimeError: wrapped C/C++ object of type QLabel has been deleted
RuntimeError: wrapped C/C++ object of type QLabel has been deleted
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\bug_reporter\tool.py", line 311, in status
self.result.setText(text)
See log for complete Python traceback.
OpenGL version: 3.3.13596 Core Profile Forward-Compatible Context 20.10.35.02 27.20.1034.6
OpenGL renderer: AMD Radeon R7 M460
OpenGL vendor: ATI Technologies Inc.
Python: 3.11.4
Locale: en_US.cp1252
Qt version: PyQt6 6.8.1, Qt 6.8.2
Qt runtime version: 6.8.2
Qt platform: windows
Manufacturer: Dell Inc.
Model: Inspiron 5570
OS: Microsoft Windows 11 Pro (Build 26100)
Memory: 8,481,943,552
MaxProcessMemory: 137,438,953,344
CPU: 8 Intel(R) Core(TM) i7-8550U CPU @ 1.80GHz
OSLanguage: en-US
Installed Packages:
alabaster: 1.0.0
appdirs: 1.4.4
asttokens: 3.0.0
babel: 2.17.0
beautifulsoup4: 4.13.3
blockdiag: 3.0.0
blosc2: 3.6.1
build: 1.2.2.post1
certifi: 2025.7.14
cftime: 1.6.4.post1
charset-normalizer: 3.4.2
ChimeraX-AddCharge: 1.5.19
ChimeraX-AddH: 2.2.7
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.6.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.20.2
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.1.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Aniso: 1.1.4
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.60.7
ChimeraX-AtomicLibrary: 14.1.19
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.3
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 3.0.0
ChimeraX-Boltz: 1.0
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.2
ChimeraX-BuildStructure: 2.13.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.5.1
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.5
ChimeraX-ChemGroup: 2.0.2
ChimeraX-Clashes: 2.3
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.8
ChimeraX-CommandLine: 1.3
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.10.1
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.5
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.4
ChimeraX-Dicom: 1.2.7
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.4
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.4.1
ChimeraX-Hbonds: 2.5.1
ChimeraX-Help: 1.3
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.3
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-KVFinder: 1.6.2
ChimeraX-Label: 1.1.14
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.3
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.2.2
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.10.1
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.16
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.19
ChimeraX-ModelPanel: 1.5.1
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-MutationScores: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.2
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.14.1
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.10
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.4
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.3
ChimeraX-ProfileGrids: 1.1.3
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.6.3
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.3.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.3
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.5.7
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.17.1
ChimeraX-Shape: 1.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.2.1
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-SimilarStructures: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.19.1
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.2.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.5.2
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.2.3
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.45.2
ChimeraX-Umap: 1.0
ChimeraX-uniprot: 2.3.1
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.4.4
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.5
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.2
comtypes: 1.4.10
contourpy: 1.3.2
coverage: 7.10.0
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.0.12
debugpy: 1.8.15
decorator: 5.2.1
docutils: 0.21.2
executing: 2.2.0
filelock: 3.18.0
fonttools: 4.59.0
funcparserlib: 2.0.0a0
glfw: 2.9.0
grako: 3.16.5
h5py: 3.14.0
html2text: 2024.2.26
idna: 3.10
ihm: 2.2
imagecodecs: 2024.6.1
imagesize: 1.4.1
iniconfig: 2.1.0
ipykernel: 6.29.5
ipython: 8.26.0
ipywidgets: 8.1.7
jedi: 0.19.1
Jinja2: 3.1.6
jupyter_client: 8.6.3
jupyter_core: 5.8.1
jupyterlab_widgets: 3.0.15
kiwisolver: 1.4.8
line_profiler: 4.2.0
lxml: 5.3.1
lz4: 4.3.2
MarkupSafe: 3.0.2
matplotlib: 3.10.1
matplotlib-inline: 0.1.7
msgpack: 1.1.0
narwhals: 2.8.0
ndindex: 1.10.0
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.11.0
numpy: 2.3.3
numpy: 1.26.4
nvidia-nvjitlink-cu12: 12.9.86
OpenMM: 8.2.0
OpenMM-CUDA-12: 8.2.0
openvr: 1.26.701
packaging: 24.2
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pickleshare: 0.7.5
pillow: 10.4.0
pip: 25.0.1
pkginfo: 1.11.1
platformdirs: 4.3.8
plotly: 6.3.1
pluggy: 1.6.0
prompt_toolkit: 3.0.51
psutil: 7.0.0
pure_eval: 0.2.3
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
Pygments: 2.18.0
pyKVFinder: 0.8.3
pynmrstar: 3.3.5
pynrrd: 1.0.0
PyOpenGL: 3.1.9
PyOpenGL-accelerate: 3.1.9
pyopenxr: 1.1.4501
pyparsing: 3.2.3
pyproject_hooks: 1.2.0
PyQt6-commercial: 6.8.1
PyQt6-Qt6: 6.8.2
PyQt6-WebEngine-commercial: 6.8.0
PyQt6-WebEngine-Qt6: 6.8.2
PyQt6_sip: 13.10.0
pytest: 8.4.1
pytest-cov: 6.2.1
python-dateutil: 2.9.0.post0
pytz: 2025.2
pywin32: 310
pyzmq: 27.0.0
qtconsole: 5.5.2
QtPy: 2.4.3
qtshim: 1.1
RandomWords: 0.4.0
requests: 2.32.3
roman-numerals-py: 3.1.0
scipy: 1.14.0
setuptools: 78.1.0
sfftk-rw: 0.8.1
six: 1.16.0
snowballstemmer: 3.0.1
sortedcontainers: 2.4.0
soupsieve: 2.7
Sphinx: 8.2.3
sphinx-autodoc-typehints: 3.1.0
sphinxcontrib-applehelp: 2.0.0
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 2.0.0
sphinxcontrib-htmlhelp: 2.1.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 2.0.0
sphinxcontrib-serializinghtml: 2.0.0
stack-data: 0.6.3
superqt: 0.7.1
tables: 3.10.2
tcia_utils: 1.5.1
tifffile: 2025.3.13
tinyarray: 1.2.4
tomlkit: 0.13.3
tornado: 6.5.1
traitlets: 5.14.3
typing_extensions: 4.14.1
tzdata: 2025.2
urllib3: 2.5.0
wcwidth: 0.2.13
webcolors: 24.11.1
wheel: 0.45.1
wheel-filename: 1.4.2
widgetsnbextension: 4.0.14
WMI: 1.5.1
Change History (4)
comment:1 by , 4 weeks ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Infrastructure |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Bug Reporter: wrapped C/C++ object of type QLabel has been deleted |
comment:2 by , 4 weeks ago
| Cc: | added; removed |
|---|---|
| Owner: | changed from to |
| Summary: | Bug Reporter: wrapped C/C++ object of type QLabel has been deleted → HBonds: TypeError: acc_phi_psi() takes 8 positional arguments but 10 were given |
The user clicked Bug Report submit and then it seems closed the bug report window. But the submit code had not yet even sent the data and was just trying to show the status message in the Bug Reporter "Contacting CGL...". I don't see any opportunity between when Submit was pressed and where the error happened for the user to close the window -- there is nothing that appears to allow the event loop to run. So possibly the user closed the Bug Reporter but it didn't respond immediately so they had time to press Submit before the the close and then the submit were handled.
I'm not going to put code in to check for that unless I see another report.
Some of the earlier errors seem more significant. Reassigning to Eric.
comment:3 by , 4 weeks ago
| Component: | Infrastructure → Structure Analysis |
|---|---|
| Status: | assigned → accepted |
| Summary: | HBonds: TypeError: acc_phi_psi() takes 8 positional arguments but 10 were given → H-Bonds: acc_phi_psi() bad number of arguments |
comment:4 by , 4 weeks ago
| Resolution: | → not a bug |
|---|---|
| Status: | accepted → closed |
Bad structure (e.g. "/A DG 4 O4' has bad number of bonds")
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*So* many errors in this one. The last one across the finish line (Bug Reporter) wins...